Microbiome Research Solutions

The complexities involved in 16S rRNA community profiling and shotgun metagenomics methods pose significant challenges for microbiome research. Significant biases can be introduced during sample preparation, DNA extraction, PCR amplification, library preparation, sequencing, and/or data interpretation. To address these biases and provide a measure of standardization within microbiome research and applications, ATCC has developed a set of mock microbial communities comprising fully sequenced, characterized strains that can be used as universal controls for assay development and optimization.

The ATCC® Microbiome Standards Collection

ATCC® Microbiome Standards allow you to optimize your metagenomics research applications with confidence, and improve the consistency and reproducibility of your data run after run. From sample collection to data analysis, ATCC offers the resources you need to optimize your microbiome research and applications, including:

What Are ATCC® Microbiome Standards?

ATCC® Microbiome Standards are fully sequenced, characterized, and authenticated mock microbial communities that mimic mixed metagenomics samples. Each community is prepared from authenticated strains that have been selected for relevant phenotypic and genomic attributes such as:

Gram stain

GC content

Genome size

Spore formation

DNA/RNA genome

Envelope

Genome shape

ITS variability

Clinical relevance

Diagnostic relevance

Aerobic/anaerobic

Ability to lyse

What’s more, these standards are the only reference materials on the market completely manufactured from high-quality ATCC® Genuine Cultures that are characterized by polyphasic testing, fully sequenced, and published in various databases. These standards enable the optimization of metagenomics workflows and microbiome research applications, providing reliable comparative data while improving assay consistency.

Choose Your Format and Level of Complexity

To best support your research, ATCC® Microbiome Standards are provided in a variety of formats and levels of complexity:

Whole cell and nucleic acid preparations

Even or staggered gDNA abundance

Low, medium, or high levels of mock community complexity

Mixtures comprising 3 to 20 strains per sample

The robust applicability of these controls, combine with ATCC’s commitment to authentication and characterization, make ATCC® Microbiome Standards the ideal tool for standardizing data from a wide range of sources and generating consensus among microbiome applications and analyses.

Improve the Consistency of your Assays

ATCC® Microbiome Standards support a broad array of applications ranging from method optimization to data interpretation, and they serve as superior controls for microbial community testing and assay development on any platform. By using ATCC® Microbiome Standards combined with the One Codex data analysis module in your research, you can compare the performance and overall accuracy of your methods and ensure the validity of your results.

Figure 1. The whole cell mock microbial communities can be used to compare different DNA extraction kits. Here, we show a proof-of-concept study. Total DNA from two aliquots of the whole cell microbiome standards was extracted using two commercial extraction kits. Following extraction, the genomic DNA was analyzed using 16S rRNA and shotgun genomic sequencing analysis on the Illumina® MiSeq® platform, and the resulting data were analyzed using the ATCC bioinformatics tool in One Codex.

Figure 2. The genomic DNA mock microbial communities can be used to compare 16S rRNA and shotgun metagenomics assays. Here, we show a proof-of-concept study. The performance and overall accuracy of the quantitative genomic DNA mock microbial communities were tested using the Illumina® MiSeq® platform, and the resulting data was analyzed using the ATCC bioinformatics tool in One Codex.

Source Standards Based on Specific Applications

Pathogen Detection

ATCC has developed a mock microbial community for clinically relevant pathogen detection in partnership with the LGC Group, an international leader in genomics, measurement standards, and reference materials. With the ATCC Metagenomic Control Material for Pathogen Detection (ATCC® MSA-4000™), you can expect:

A combination of strains observed in clinical infections, including antimicrobial-resistant organisms

Absolute quantification of genomic DNA and assignment of genome copy number using Droplet Digital™ PCR to improve analytical precision

■ Staphylococcus aureus subsp. aureus (MRSA)

■ Staphylococcus aureus subsp. aureus (MSSA)

■ Streptococcus pneumoniae

■ Streptococcus pyogenes

■ Streptococcus agalactiae

■ Enterococcus faecalis

■ Pseudomonas aeruginosa

■Klebsiella pneumoniae subsp. pneumoniae

■Acinetobacter baumannii

■Escherichia coli

■Neisseria meningitidis

Figure 3. The ATCC Metagenomic Control Material for Pathogen Detection (ATCC® MSA-4000™) can be used to compare various molecular diagnostic methods. Here, we used the (A) control material to evaluate (B) digital PCR and compare (C) 16S rRNA and shotgun metagenomics analysis methods. *The percent relative abundance of Staphylococcus aureus includes both MRSA and MSSA.

Environmental Testing

The ABRF-MGRG metagenomics reference standards were developed and packaged in partnership with the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF-MGRG) as part of the Extreme Microbiome Project (XMP). With the ABRF-MGRG metagenomics reference standards (ATCC®MSA-3000™, MSA-3001™, MSA-3002™), you can expect:

Access to One Codex, the leading bioinformatics platform for microbial genomics

■ Enterococcus faecalis

■ Staphylococcus epidermidis

■ Micrococcus luteus

■ Haloferax volcanii

■ Halobacillus halophilus

■ Bacillus subtilis

■ Pseudoalteromonas haloplanktis

■ Escherichia coli

■ Chromobacterium violaceum

■ Pseudomonas fluorescens

Figure 4. The ABRF-MGRG metagenomics reference standards can be used to compare different sequencing platforms. As a proof-of-concept, ATCC® MSA-3001™ was used a control material to compare the performance of the Illumina® MiniSeq™, MiSeq®, NextSeq®, and HiSeq® platforms. Data were analyzed using the ATCC bioinformatics tool in One Codex. ABRF-MGRG metagenomics reference standards can also be used to evaluate run-to-run reproducibility (data not shown).

Calibrate your Experiments with Spike-in Controls

Microbiome spike-in controls from ATCC comprise exogenous bacteria and archaea that do not exist in the human microbiome under physiological conditions, making them easy to distinguish from human bacteria via standard sequencing methods. These microbiome standards offer a valuable way to evaluate the accuracy and reproducibility of library preparation, sequencing, and data analysis in both 16S rRNA community profiling and shotgun metagenomics. Further, they enable inter-sample comparison, thereby providing a way to standardize microbiome research across different laboratories.

Genus

Expected

Unspiked Control

Spiked

Staphylococcus

10.00%

18.94%

20.30%

Enterococcus

10.00%

13.13%

13.41%

Streptococcus

10.00%

11.87%

9.01%

Lactobacillus

10.00%

10.65%

8.57%

Escherichia

10.00%

10.06%

8.23%

Bacillus

10.00%

7.49%

7.42%

Deinococcus

10.00%

10.16%

7.34%

Bifidobacterium

10.00%

6.72%

6.66%

Clostridium

10.00%

8.23%

5.27%

Rhodobacter

10.00%

2.76%

3.14%

Spike-in strain 1

0.00%

0.00%

7.67%

Spike-in strain 2

0.00%

0.00%

1.60%

Spike-in strain 3

0.00%

0.00%

1.36%

Figure 5. Microbiome spike-in controls are ideal for evaluating the accuracy and reproducibility of different sequencing methods. As a proof-of-concept, 1 μL of the spike-in control (1 x 106 genomes/strain) was added to 20 μL of the 10 strain even mix genomic material standard (ATCC® MSA-1000™). Samples were then evaluated using 16S rRNA community profiling. The percentage of reads recovered were determined using the One Codex database. Strains were evaluated at the genus level.

Disease State Microbiome

Can’t find the pre-mixed microbiome standards that you need for your disease-state research? ATCC has a wide assortment of cultures and nucleic acids to choose from when validating microbiome applications, such as library preparation and next-generation sequencing, including individual strains related to:

LGC Metagenomic Control Materials

ATCC has partnered with the LGC Group, the UK’s designated National Measurement Institute for chemical and bioanalytical measurements and an international leader in the laboratory services, measurement standards, reference materials, genomics and proficiency testing marketplaces, to develop metagenomic control materials for clinically relevant pathogen detection. Each product comprises genomic DNA prepared from ATCC® Genuine Cultures and quantitated using Droplet Digital™ PCR.